With rising interest in marine renewable energy (MRE) associated with offshore wind, waves, and tidal flows, the effects of device placement on changes in animal behaviour require proper assessment to minimise environmental impacts and inform decision making. High-frequency multibeam echosounders, or imaging sonars, can be used to observe and record the underwater movement and behaviour of animals at a fine scale (tens of metres). However, robust target detection and tracking of closely spaced animals are required for assessing animal–device and predator–prey interactions. Dual-frequency multibeam echosounders combine longer detection ranges (low frequency) with greater detail (high frequency) while maintaining a wide field of view and a full water column range compared to acoustic or optical cameras. This study evaluates the performance of the Tritech Gemini 1200ik imaging sonar at 720 kHz (low frequency) and 1200 kHz (high frequency) for small target detection with increasing range and the ability of the two frequency modes to discriminate between two closely spaced targets using a 38.1 mm tungsten carbide acoustic calibration sphere under controlled conditions. The quality of target detection decreases for both modes with increasing range, with a 25 m limit of detection at high frequency and a low-frequency mode able to detect the target up to 30 m under test conditions in shallow water. We quantified the enhanced performance of the high-frequency mode in discriminating targets at short ranges and improved target detection and discrimination at high ranges in the low-frequency mode.